Objective: To explore the mechanism of shadow bands on denaturing PAGE for PCR products of STR sequences and try to eliminate them.
Methods: PCR and asymmetric PCR were employed. The amplified fragments were separated on denaturing PAGE and visualized by silver stain.
Results: By asymmetric PCR, half of shadow bands of dinucleotide repeats were eliminated and there was only one band for each allele for tetranucleotide sequence. A different migration between the sense strand and antisense strand was identified.
Conclusion: The difference between sense and antisense strands in electrophoresis is one of the causes in shadow bands, and these shadow bands can be eliminated by asymmetric PCR partly or totally.